Error installng bcftools-1.4

Question

[abdulbenissa]

Hello Everyone

I am trying to install bcftools1-4 on my MAC but for some reason is giving me this error I had followed exact documentations I have installed and unzipped in /usr/local/bin , yet I have this lzma.h fie which I dont know how to deal with, bcftools-1.3 was working fine with me on same machine , I hope is not bad Idea to update it !! then done the fowlloing :

./configure make

cram/cram_io.c:60:10: fatal error: 'lzma.h' file not found
#include <lzma.h>
         ^
1 error generated.
make[1]: *** [cram/cram_io.o] Error 1
make: *** [htslib-1.4/libhts.a] Error 2

[abdulbenissa]

Sir Many thanks for your reply but I think I have all those libraries ?!

/usr/local/bin/xz

/usr/bin/bzip2

the zlib is already included in the OS I believe ?!

even when I tried ti Install it by brew I got this

####MPro-2:~ MyMac$ brew install zlib
Warning: zlib is a keg-only and another version is linked to opt.
Use `brew install --force` if you want to install this version

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

[abdulbenissa]

As Mr. Lindenbaum recommended, this thread

it worked well now thanks again. even when I had xz library in the correct location. I had to disconnect then connected again utilizing brew, after that the compiler didnt request the lzmah.h library again. and bcfrools1-4 is working fine ..

Best

Answer 1

[Pierre Lindenbaum]

https://github.com/samtools/samtools/blob/develop/INSTALL

Samtools requires the zlib library <http://zlib.net>, the bzip2
library <http://bzip.org/>, **liblzma** <http://tukaani.org/xz/> and (optionally)
a curses or GNU ncurses library <http://www.gnu.org/software/ncurses/>.

https://tukaani.org/xz/

[abdulbenissa]

Sir Many thanks for your reply but I think I have all those libraries ?!

/usr/local/bin/xz

/usr/bin/bzip2

the zlib is already included in the OS I believe ?!

even when I tried ti Install it by brew I got this

MPro-2:~ MyMac$ brew install zlib

Warning: zlib is a keg-only and another version is linked to opt. Use brew install --force if you want to install this version

[GenoMax]

It appears that you need to install package xz for macOS. See this thread for more information.

Answer 2

[James Bonfield]

If you're really struggling and don't mind being unable to read some CRAM files then build htslib first using --disable-lzma.

You have the command line tools for xz, bzip2, but I assume not the development libraries. I don't know what packages they're called on the Mac, but it's typically something like libbz2-devel or -dev and maybe the xz or xz-utils package for lzma.h. Do a google search for those headers and you'll find them.